Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo)
Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo)
Using package Chemical with version 1.4.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo)
Running command: translateModel(Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
translateModel(Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo): time 0.1054/0.1054, allocations: 15.26 MB / 31.21 MB, free: 3.223 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.0009885/0.0009885, allocations: 174.1 kB / 36.29 MB, free: 2.262 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.613/1.613, allocations: 223.3 MB / 264.5 MB, free: 5.801 MB / 202.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0007975/0.0007975, allocations: 98.08 kB / 319.9 MB, free: 2.75 MB / 250.7 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 0.000393/0.000393, allocations: 17.88 kB / 385.2 MB, free: 50.72 MB / 298.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1065/0.1069, allocations: 54.63 MB / 439.8 MB, free: 15.96 MB / 314.7 MB
Notification: Performance of FrontEnd - scodeFlatten: time 0.3881/0.495, allocations: 100.3 MB / 0.5274 GB, free: 15.68 MB / 378.7 MB
Notification: Performance of FrontEnd - mkProgramGraph: time 0.0002425/0.4953, allocations: 68.64 kB / 0.5275 GB, free: 15.68 MB / 378.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:4721:7-4721:66:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System solution.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Solution.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System CH4.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$CH4.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System CO2.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$CO2.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System H2O.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$H2O.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System H2.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$H2.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
Notification: Performance of FrontEnd - DAE generated: time 0.1149/0.6102, allocations: 48.3 MB / 0.5747 GB, free: 20.21 MB / 394.7 MB
Notification: Performance of FrontEnd: time 2.585e-06/0.6103, allocations: 0 / 0.5747 GB, free: 20.21 MB / 394.7 MB
Notification: Performance of Transformations before backend: time 0.0001084/0.6104, allocations: 23.38 kB / 0.5747 GB, free: 20.21 MB / 394.7 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 276
 * Number of variables: 276
Notification: Performance of Generate backend data structure: time 0.004301/0.6147, allocations: 1.655 MB / 0.5763 GB, free: 19.07 MB / 394.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.857e-05/0.6148, allocations: 16.45 kB / 0.5763 GB, free: 19.07 MB / 394.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001539/0.6163, allocations: 327.8 kB / 0.5766 GB, free: 18.93 MB / 394.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.002425/0.6188, allocations: 0.9384 MB / 0.5775 GB, free: 18.39 MB / 394.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001687/0.619, allocations: 108.8 kB / 0.5777 GB, free: 18.36 MB / 394.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0004231/0.6194, allocations: 112.5 kB / 0.5778 GB, free: 18.36 MB / 394.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.00379/0.6232, allocations: 1.982 MB / 0.5797 GB, free: 17.9 MB / 394.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 3.25e-05/0.6233, allocations: 3.938 kB / 0.5797 GB, free: 17.9 MB / 394.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 9.664e-05/0.6234, allocations: 40.44 kB / 0.5797 GB, free: 17.9 MB / 394.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.404e-05/0.6234, allocations: 27.12 kB / 0.5798 GB, free: 17.9 MB / 394.7 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.003217/0.6266, allocations: 2.832 MB / 0.5825 GB, free: 17.49 MB / 394.7 MB
Warning: The model contains alias variables with redundant start and/or conflicting nominal values. It is recommended to resolve the conflicts, because otherwise the system could be hard to solve. To print the conflicting alias sets and the chosen candidates please use -d=aliasConflicts.
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.008627/0.6353, allocations: 5.74 MB / 0.5881 GB, free: 15.03 MB / 394.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.003294/0.6386, allocations: 2.803 MB / 0.5909 GB, free: 13.48 MB / 394.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.001106/0.6397, allocations: 1.001 MB / 0.5918 GB, free: 12.95 MB / 394.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.0004844/0.6402, allocations: 331.4 kB / 0.5922 GB, free: 12.8 MB / 394.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.738e-05/0.6403, allocations: 51.62 kB / 0.5922 GB, free: 12.75 MB / 394.7 MB
Notification: Performance of pre-optimization done (n=129): time 4.328e-06/0.6403, allocations: 0 / 0.5922 GB, free: 12.75 MB / 394.7 MB
Notification: Performance of matching and sorting (n=170): time 0.02504/0.6653, allocations: 8.431 MB / 0.6004 GB, free: 4.727 MB / 394.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.28e-05/0.6654, allocations: 73.41 kB / 0.6005 GB, free: 4.641 MB / 394.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.001292/0.6667, allocations: 0.7506 MB / 0.6013 GB, free: 3.883 MB / 394.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0002665/0.667, allocations: 57.7 kB / 0.6013 GB, free: 3.82 MB / 394.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004293/0.6675, allocations: 461.2 kB / 0.6017 GB, free: 3.363 MB / 394.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.000753/0.6682, allocations: 0.5659 MB / 0.6023 GB, free: 2.789 MB / 394.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001169/0.6684, allocations: 32 kB / 0.6023 GB, free: 2.758 MB / 394.7 MB
Notification: Performance of setup shared object (initialization): time 0.0002325/0.6686, allocations: 365.8 kB / 0.6027 GB, free: 2.395 MB / 394.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.002239/0.6709, allocations: 0.9839 MB / 0.6036 GB, free: 1.41 MB / 394.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.001769/0.6727, allocations: 1.162 MB / 0.6048 GB, free: 220 kB / 394.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003333/0.676, allocations: 2.245 MB / 0.607 GB, free: 13.93 MB / 410.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 7.434e-06/0.676, allocations: 0 / 0.607 GB, free: 13.93 MB / 410.7 MB
Notification: Performance of matching and sorting (n=191) (initialization): time 0.007128/0.6832, allocations: 2.818 MB / 0.6097 GB, free: 11.09 MB / 410.7 MB
Notification: Performance of prepare postOptimizeDAE: time 4.263e-05/0.6833, allocations: 4.406 kB / 0.6097 GB, free: 11.09 MB / 410.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.892e-05/0.6833, allocations: 7.938 kB / 0.6097 GB, free: 11.08 MB / 410.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.003169/0.6865, allocations: 469.9 kB / 0.6102 GB, free: 10.61 MB / 410.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.00215/0.6886, allocations: 347.5 kB / 0.6105 GB, free: 10.27 MB / 410.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.007096/0.6958, allocations: 4.379 MB / 0.6148 GB, free: 5.602 MB / 410.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.00174/0.6976, allocations: 71.88 kB / 0.6149 GB, free: 5.531 MB / 410.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0003771/0.698, allocations: 59.97 kB / 0.6149 GB, free: 5.473 MB / 410.7 MB
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 14
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (177):
 * Single equations (assignments): 174
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (linear and non-linear blocks): 0
 * Torn equation systems: 3
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems: 1 {(1,100.0%) 3}
 * Non-linear torn systems: 2 {1 8,1 3}
Notification: Performance of prepare postOptimizeDAE: time 0.001205/0.6992, allocations: 294.1 kB / 0.6152 GB, free: 5.176 MB / 410.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0004756/0.6997, allocations: 114.6 kB / 0.6153 GB, free: 5.062 MB / 410.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.007549/0.7072, allocations: 2.953 MB / 0.6182 GB, free: 2.086 MB / 410.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.569e-05/0.7073, allocations: 20 kB / 0.6182 GB, free: 2.066 MB / 410.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.07e-05/0.7073, allocations: 0 / 0.6182 GB, free: 2.066 MB / 410.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 2.42e-05/0.7074, allocations: 7.969 kB / 0.6182 GB, free: 2.059 MB / 410.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.01202/0.7194, allocations: 6.012 MB / 0.6241 GB, free: 11.9 MB / 426.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.563e-05/0.7195, allocations: 4 kB / 0.6241 GB, free: 11.9 MB / 426.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001761/0.7212, allocations: 344.2 kB / 0.6244 GB, free: 11.56 MB / 426.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.002933/0.7242, allocations: 466 kB / 0.6249 GB, free: 11.1 MB / 426.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0001849/0.7244, allocations: 55.92 kB / 0.6249 GB, free: 11.05 MB / 426.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.006329/0.7308, allocations: 4.318 MB / 0.6291 GB, free: 6.434 MB / 426.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 9.598e-06/0.7308, allocations: 16 kB / 0.6291 GB, free: 6.418 MB / 426.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.009026/0.7398, allocations: 4.394 MB / 0.6334 GB, free: 1.926 MB / 426.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.000497/0.7404, allocations: 191.6 kB / 0.6336 GB, free: 1.719 MB / 426.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0003291/0.7407, allocations: 47.92 kB / 0.6337 GB, free: 1.672 MB / 426.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001127/0.7419, allocations: 59.89 kB / 0.6337 GB, free: 1.613 MB / 426.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0003099/0.7422, allocations: 141 kB / 0.6339 GB, free: 1.477 MB / 426.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001356/0.7424, allocations: 55.98 kB / 0.6339 GB, free: 1.422 MB / 426.7 MB
Notification: Performance of sorting global known variables: time 0.0008714/0.7432, allocations: 0.5264 MB / 0.6344 GB, free: 0.8945 MB / 426.7 MB
Notification: Performance of sort global known variables: time 2.4e-07/0.7432, allocations: 0 / 0.6344 GB, free: 0.8945 MB / 426.7 MB
Notification: Performance of remove unused functions: time 0.00334/0.7466, allocations: 0.8001 MB / 0.6352 GB, free: 96 kB / 426.7 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 25
 * Number of states: 5 (solution.temperature,CH4.logn,CO2.logn,H2O.logn,H2.logn)
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (173):
 * Single equations (assignments): 170
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (linear and non-linear blocks): 0
 * Torn equation systems: 3
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems: 1 {(1,100.0%) 3}
 * Non-linear torn systems: 2 {1 3,1 8}
Notification: Performance of Backend phase and start with SimCode phase: time 0.002483/0.7491, allocations: 0.8949 MB / 0.6361 GB, free: 15.19 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.004465/0.7536, allocations: 2.595 MB / 0.6386 GB, free: 12.57 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.045e-05/0.7536, allocations: 4 kB / 0.6386 GB, free: 12.57 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.00245/0.7561, allocations: 1.474 MB / 0.6401 GB, free: 11.07 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003081/0.7592, allocations: 396.2 kB / 0.6404 GB, free: 10.69 MB / 442.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.006155/0.7653, allocations: 3.581 MB / 0.6439 GB, free: 7.004 MB / 442.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0009606/0.7663, allocations: 1.149 MB / 0.6451 GB, free: 5.824 MB / 442.7 MB
Notification: Performance of simCode: alias equations: time 0.00129/0.7676, allocations: 229.7 kB / 0.6453 GB, free: 5.598 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000439/0.7681, allocations: 123.4 kB / 0.6454 GB, free: 5.477 MB / 442.7 MB
Notification: Performance of SimCode: time 1.072e-06/0.7681, allocations: 3.938 kB / 0.6454 GB, free: 5.473 MB / 442.7 MB
Notification: Performance of Templates: time 0.05444/0.8225, allocations: 32.34 MB / 0.677 GB, free: 5.355 MB / 474.7 MB
make -j1 -f Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.makefile
(rm -f Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; mkfifo Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe ; head -c 1048576 < Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe >> ../files/Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.sim & ./Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.ClimateChange.HydrogenotrophicMethanogenesis.pipe 2>&1)